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CellPhoneDB for scanpy

Usage:

import cellphonedb as cphdb
outs=cphdb.statistical_analysis_scanpy(adata, adata.var_names, adata.obs_names, obs_key)

obs_key must be some key in adata.obs that groups the cells, such as 'celltype', 'louvain' or 'cluster'.

There is a jupyter notebook in here somewhere which shows that this works fine.

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  • Python 85.9%
  • Jupyter Notebook 12.7%
  • R 1.2%
  • Other 0.2%